The small subunit rRNA (SSrRNA) genes of six marine oligohymenophoreans, namely Uronemella filificum Schizocalyptra sp.-WYG07060701, Schizocalyptra aeschtae Pleuronema Sinica P. czapikae and Paratetrahymenasp., were sequenced. Phylogenetic trees were constructed with four different methods to assess the inter- and intrageneric relationships among the scuticociliates and the phylogenetic assignment of the order Loxocephalida. The SSrRNA phylogeny indicates that: (i) Paratetrahymena is most closely related to Cardiostomatella (ii) the order Loxocephalida and the family Uronematidae both appear to be polyphyletic; (iii) the order Philasterida is a well-defined taxon; (iv) Cyclidium porcatum falls outside the order Pleuronematida in all analyses; (v) the validity of the genus Uronemella is confirmed; (vi) Schizocalyptra is a member of the family Pleuronematidae. Furthermore, the predicted secondary structures of the variable region 4 of the SSrRNA gene sequences show that the size of the terminal bulge in Helix E23–7 is probably different for the orders Philasterida and Pleuronematida. Also, compared to Uronema and Homalogastra Uronemella
has distinct patterns in Helices E23–1, E23–7, E23–8 and E23–9.